Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold33
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2032796
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 48244 characters in sequence are not A, C, G, or T
File 8 of 13
Found at i:1081330 original size:52 final size:51
Alignment explanation
Indices: 1081207--1081372 Score: 192
Period size: 52 Copynumber: 3.2 Consensus size: 51
1081197 CATAATCGAC
* * *
1081207 GATACTCCAACCCCAGTTTTA-TTTCTAAAACACTAATTTTCCACAATCGGG
1 GATACTCCAACCCGA-TTTTATTTTCAAAAACACCAATTTTCCACAATCGGG
* * **
1081258 GATACTTCAACCCCGGTTTTATTTTC-AAAACACCAATTTTCCTTTAATCGGG
1 GATACTCCAA-CCCGATTTTATTTTCAAAAACACCAATTTTCC-ACAATCGGG
* * *
1081310 GATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAG
1 GATACTCCAAC-CCGATTTTATTTTCAAAAACACCAATTTTCCACAATCGGG
1081362 GATACTCCAAC
1 GATACTCCAAC
1081373 GTCGTTATTT
Statistics
Matches: 97, Mismatches: 13, Indels: 9
0.82 0.11 0.08
Matches are distributed among these distances:
51 30 0.31
52 52 0.54
53 15 0.15
ACGTcount: A:0.31, C:0.27, G:0.10, T:0.32
Consensus pattern (51 bp):
GATACTCCAACCCGATTTTATTTTCAAAAACACCAATTTTCCACAATCGGG
Found at i:1081517 original size:79 final size:78
Alignment explanation
Indices: 1081387--1081619 Score: 254
Period size: 79 Copynumber: 2.9 Consensus size: 78
1081377 TTATTTCATC
** * *
1081387 GGGGATACTCC-ACCCCGTTACCTCCGAGTGGATACTCCAACCCCGGCTTTATTTTCAAAATATT
1 GGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCC-GTTTTATTTTCAAAATATT
*
1081451 GATTTCTCATAATT
65 GATTTCTCATAACT
* ** **
1081465 GGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAATCTTGATTTTA-TTTCCTAATCAT
1 GGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCG-TTTTATTTTCAAAAT-AT
* * *
1081529 CGATTTTTCACAACT
64 TGATTTCTCATAACT
* * *
1081544 GGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCCCGTTATTATCTTCAAAATATT
1 GGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGTT-TTATTTTCAAAATATT
*
1081609 AAATTTCTCAT
65 -GATTTCTCAT
1081620 CGGGACATAT
Statistics
Matches: 124, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
78 21 0.17
79 90 0.73
80 13 0.10
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (78 bp):
GGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGTTTTATTTTCAAAATATTG
ATTTCTCATAACT
Found at i:1084016 original size:137 final size:138
Alignment explanation
Indices: 1083769--1084045 Score: 484
Period size: 137 Copynumber: 2.0 Consensus size: 138
1083759 ATCAGTATCT
* *
1083769 TCACGAAACACGGGCTCTGATACCAACTGTTACGGGCCTGGACTTTAGCCTAGCAAATCGCGCGG
1 TCACGAAACACGGACTCTGATACCAACTGTTACGGGCCTGGACTTTAGCCTAGCAAATCGCGCGA
*
1083834 CCTTAGGCTTGGAAATCACTTCCTTATATGCCTAAGTCAGCCTTTAAACACTAAAAAAAAGAAAA
66 CCTTAGGCTTGGAAATCACTTCCTTATATGCCTAAGTCAACCTTTAAACACTAAAAAAAAGAAAA
*
1083899 CTCTGAGG
131 CTCTAAGG
*
1083907 TCACGAAACATGGACTCTGATA-CAACTGTTACGGGCCTGGACTTTAGCCTAGCAAATCGCGCGA
1 TCACGAAACACGGACTCTGATACCAACTGTTACGGGCCTGGACTTTAGCCTAGCAAATCGCGCGA
* *
1083971 CCTTAGGCTTGGAAATCACTTCCTTATATGCCTCAGTCAACCTTTAAACACTAAAAAAAAGGAAA
66 CCTTAGGCTTGGAAATCACTTCCTTATATGCCTAAGTCAACCTTTAAACACTAAAAAAAAGAAAA
1084036 CTCTAAGG
131 CTCTAAGG
1084044 TC
1 TC
1084046 CCTAAGGTAC
Statistics
Matches: 132, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
137 112 0.85
138 20 0.15
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (138 bp):
TCACGAAACACGGACTCTGATACCAACTGTTACGGGCCTGGACTTTAGCCTAGCAAATCGCGCGA
CCTTAGGCTTGGAAATCACTTCCTTATATGCCTAAGTCAACCTTTAAACACTAAAAAAAAGAAAA
CTCTAAGG
Found at i:1086836 original size:32 final size:33
Alignment explanation
Indices: 1086762--1086836 Score: 100
Period size: 32 Copynumber: 2.3 Consensus size: 33
1086752 TTATATTTAA
* *
1086762 AATATTTTATATTTATATAAATTTTGATATATT
1 AATATTTTATATTTATATAAATTTTAAAATATT
1086795 AATGA-TTTATA-TTATATAAATTTTAAAATATT
1 AAT-ATTTTATATTTATATAAATTTTAAAATATT
*
1086827 TATATTTTAT
1 AATATTTTAT
1086837 TTCATGTTCA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
31 1 0.03
32 26 0.70
33 9 0.24
34 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (33 bp):
AATATTTTATATTTATATAAATTTTAAAATATT
Found at i:1088357 original size:24 final size:24
Alignment explanation
Indices: 1088330--1088377 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1088320 TTTATGCCTC
* *
1088330 AACTTAATTTAATTTAATACGATT
1 AACTTAACTTAATTTAACACGATT
*
1088354 AACTTAACTTAATTTGACACGATT
1 AACTTAACTTAATTTAACACGATT
1088378 TATTATTATG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.40, C:0.12, G:0.06, T:0.42
Consensus pattern (24 bp):
AACTTAACTTAATTTAACACGATT
Found at i:1088547 original size:17 final size:18
Alignment explanation
Indices: 1088503--1088547 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 18
1088493 AAATGGATTT
*
1088503 ATATATTAATAATAAATA
1 ATATATTAACAATAAATA
1088521 ATTAATATTAACAA-AAATA
1 A-T-ATATTAACAATAAATA
1088540 ATATATTA
1 ATATATTA
1088548 TATTATTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
17 6 0.25
18 2 0.08
19 7 0.29
20 9 0.38
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (18 bp):
ATATATTAACAATAAATA
Found at i:1088603 original size:29 final size:29
Alignment explanation
Indices: 1088571--1088631 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
1088561 ATAAATATTT
* *
1088571 ATAAAAT-ATTATTTTTGAATAATTTTTTA
1 ATAAAATAAATATATTT-AATAATTTTTTA
* *
1088600 ATAATATAAATATATTTAATTATTTTTTA
1 ATAAAATAAATATATTTAATAATTTTTTA
1088629 ATA
1 ATA
1088632 TTTCAAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 20 0.74
30 7 0.26
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (29 bp):
ATAAAATAAATATATTTAATAATTTTTTA
Found at i:1089076 original size:22 final size:23
Alignment explanation
Indices: 1089029--1089097 Score: 74
Period size: 22 Copynumber: 3.1 Consensus size: 23
1089019 TGATATCTAT
*
1089029 TTAATTA-AAAAATTATTTAA-A
1 TTAATTATAAAAATTATATAATA
1089050 TTTAATTATAAAAA-TATATAATA
1 -TTAATTATAAAAATTATATAATA
*
1089073 TTAA-TATAAAATATTTTATAATA
1 TTAATTATAAAA-ATTATATAATA
1089096 TT
1 TT
1089098 TTAATATATT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
21 7 0.17
22 18 0.44
23 16 0.39
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
TTAATTATAAAAATTATATAATA
Found at i:1089097 original size:10 final size:9
Alignment explanation
Indices: 1089081--1089114 Score: 50
Period size: 10 Copynumber: 3.6 Consensus size: 9
1089071 TATTAATATA
1089081 AAATATTTT
1 AAATATTTT
1089090 ATAATATTTT
1 A-AATATTTT
1089100 AATATATTTT
1 AA-ATATTTT
1089110 AAATA
1 AAATA
1089115 ATAAAATAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 5 0.22
10 18 0.78
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (9 bp):
AAATATTTT
Found at i:1090488 original size:20 final size:20
Alignment explanation
Indices: 1090444--1090497 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
1090434 CTATCATTGT
*
1090444 TTGTATCGATACATGGTACA
1 TTGTATCGATACATGATACA
*
1090464 ATGTATCGATACATGATGA-A
1 TTGTATCGATACATGAT-ACA
*
1090484 TTGTATCGAGACAT
1 TTGTATCGATACAT
1090498 TGCTTGTAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 28 0.97
21 1 0.03
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.33
Consensus pattern (20 bp):
TTGTATCGATACATGATACA
Found at i:1098577 original size:22 final size:22
Alignment explanation
Indices: 1098552--1098629 Score: 120
Period size: 22 Copynumber: 3.5 Consensus size: 22
1098542 AGATTTGACA
* *
1098552 AAGGGGGAGAAATGCCTTGATT
1 AAGGGGGAGAAATTCTTTGATT
1098574 AAGGGGGAGAAATTCTTTGATT
1 AAGGGGGAGAAATTCTTTGATT
* *
1098596 AAGGCGGAGAAATTCTTTAATT
1 AAGGGGGAGAAATTCTTTGATT
1098618 AAGGGGGAGAAA
1 AAGGGGGAGAAA
1098630 AATGAAAACT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.36, C:0.06, G:0.33, T:0.24
Consensus pattern (22 bp):
AAGGGGGAGAAATTCTTTGATT
Found at i:1100937 original size:2 final size:2
Alignment explanation
Indices: 1100930--1100962 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1100920 AGCGTAAGTT
1100930 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1100963 TTCTTTGGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1103134 original size:2 final size:2
Alignment explanation
Indices: 1103123--1103161 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
1103113 AGCTAGGAAC
1103123 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1103162 GTACTATAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1104486 original size:2 final size:2
Alignment explanation
Indices: 1104479--1104511 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1104469 TTCTCTGATG
1104479 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1104512 ACATTAGCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1108276 original size:23 final size:21
Alignment explanation
Indices: 1108234--1108277 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 21
1108224 TTTAAAAAAT
* *
1108234 TATATTAAATATTTATATTTA
1 TATATTAAATAATTAAATTTA
1108255 TATATCTATAATAATTAAATTTA
1 TATAT-TA-AATAATTAAATTTA
1108278 AATAAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 5 0.26
22 2 0.11
23 12 0.63
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
TATATTAAATAATTAAATTTA
Found at i:1108801 original size:2 final size:2
Alignment explanation
Indices: 1108749--1108783 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1108739 TATGTTTCAA
1108749 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1108784 AAACATTACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1108948 original size:2 final size:2
Alignment explanation
Indices: 1108941--1108968 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1108931 ACGTAATAAC
1108941 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1108969 TGTAAAAGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1109584 original size:2 final size:2
Alignment explanation
Indices: 1109577--1109611 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1109567 CATGATTCAT
* *
1109577 TA TA TA TA TA TA TA TA TA TA TA TA CA CA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1109612 GGTTTATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1111317 original size:2 final size:2
Alignment explanation
Indices: 1111310--1111336 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1111300 ATTGCATTGA
1111310 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1111337 AAGTAATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1113396 original size:21 final size:21
Alignment explanation
Indices: 1113372--1113418 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
1113362 ATAAAATTAG
*
1113372 ATAT-ATGAAATCTAAAGTTTA
1 ATATCATG-AATCTAAAGGTTA
*
1113393 ATATCTTGAATCTAAAGGTTA
1 ATATCATGAATCTAAAGGTTA
1113414 ATATC
1 ATATC
1113419 TTGATATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 21 0.91
22 2 0.09
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.38
Consensus pattern (21 bp):
ATATCATGAATCTAAAGGTTA
Found at i:1113419 original size:21 final size:21
Alignment explanation
Indices: 1113380--1113422 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1113370 AGATATATGA
*
1113380 AATCTAAAGTTTAATATCTTG
1 AATCTAAAGGTTAATATCTTG
1113401 AATCTAAAGGTTAATATCTTG
1 AATCTAAAGGTTAATATCTTG
1113422 A
1 A
1113423 TATTATATGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.40
Consensus pattern (21 bp):
AATCTAAAGGTTAATATCTTG
Found at i:1115622 original size:13 final size:13
Alignment explanation
Indices: 1115604--1115632 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1115594 CAACGTCATA
1115604 AAAATATTACAAG
1 AAAATATTACAAG
1115617 AAAATATTACAAG
1 AAAATATTACAAG
1115630 AAA
1 AAA
1115633 GACAAGAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.66, C:0.07, G:0.07, T:0.21
Consensus pattern (13 bp):
AAAATATTACAAG
Found at i:1115955 original size:20 final size:22
Alignment explanation
Indices: 1115911--1115955 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
1115901 TAATTTATAA
*
1115911 TAAATCAAAAATTATTAACATT
1 TAAATCAAAAATTATTAACACT
*
1115933 TAAAT-AAAAATT-TTAAGACT
1 TAAATCAAAAATTATTAACACT
1115953 TAA
1 TAA
1115956 TTAATTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 9 0.43
21 7 0.33
22 5 0.24
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.36
Consensus pattern (22 bp):
TAAATCAAAAATTATTAACACT
Found at i:1116056 original size:20 final size:18
Alignment explanation
Indices: 1116013--1116048 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1116003 TGTGTGTGCT
1116013 TGTGTATATATATATATA
1 TGTGTATATATATATATA
*
1116031 TGTGTATATTTATATATA
1 TGTGTATATATATATATA
1116049 GCTGTGTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (18 bp):
TGTGTATATATATATATA
Found at i:1116827 original size:2 final size:2
Alignment explanation
Indices: 1116814--1116848 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1116804 AAAATGTACT
*
1116814 TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1116849 GATAATGCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1117232 original size:20 final size:21
Alignment explanation
Indices: 1117209--1117250 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1117199 TATCATTAAT
1117209 ATAATATA-TATAAAATAAAA
1 ATAATATATTATAAAATAAAA
*
1117229 ATAATATATTATATAATAAAA
1 ATAATATATTATAAAATAAAA
1117250 A
1 A
1117251 ATACTAGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
ATAATATATTATAAAATAAAA
Found at i:1122850 original size:11 final size:12
Alignment explanation
Indices: 1122819--1122874 Score: 55
Period size: 11 Copynumber: 4.8 Consensus size: 12
1122809 TAAATTTTAA
1122819 TATATTTATATAT
1 TATA-TTATATAT
1122832 TCATATTATATAT
1 T-ATATTATATAT
*
1122845 TA-ATTAT-TTT
1 TATATTATATAT
1122855 TATATTATAT-T
1 TATATTATATAT
*
1122866 TTTATTATA
1 TATATTATA
1122875 AAATTATATC
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
10 4 0.11
11 19 0.50
12 2 0.05
13 10 0.26
14 3 0.08
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (12 bp):
TATATTATATAT
Found at i:1122858 original size:15 final size:13
Alignment explanation
Indices: 1122819--1122870 Score: 52
Period size: 13 Copynumber: 3.8 Consensus size: 13
1122809 TAAATTTTAA
*
1122819 TATATTTATATAT
1 TATATTTTTATAT
*
1122832 TCATA-TTATATAT
1 T-ATATTTTTATAT
1122845 TAATTATTTTTATAT
1 T-A-TATTTTTATAT
1122860 TATATTTTTAT
1 TATATTTTTAT
1122871 TATAAAATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
13 20 0.59
14 6 0.18
15 8 0.24
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (13 bp):
TATATTTTTATAT
Found at i:1123320 original size:23 final size:22
Alignment explanation
Indices: 1123291--1123364 Score: 73
Period size: 23 Copynumber: 3.3 Consensus size: 22
1123281 TTAATTTTTT
1123291 TTTATTTTTAAAATTTTAAATTA
1 TTTATTTTTAAAATTTT-AATTA
* *
1123314 TTTATTTTCATAA-TTTAA-TA
1 TTTATTTTTAAAATTTTAATTA
1123334 TTT-TTATTTAAAATTTTTTAATTA
1 TTTATT-TTTAAAA--TTTTAATTA
1123358 TTTATTT
1 TTTATTT
1123365 ATTCAATATG
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
19 2 0.05
20 10 0.24
21 2 0.05
22 3 0.07
23 16 0.39
24 6 0.15
25 2 0.05
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (22 bp):
TTTATTTTTAAAATTTTAATTA
Found at i:1123361 original size:22 final size:22
Alignment explanation
Indices: 1123297--1123365 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 22
1123287 TTTTTTTATT
*
1123297 TTTAAAA-TTTTAAATTATTTA
1 TTTAAAATTTTTTAATTATTTA
* **
1123318 TTTTCATAATTTAAT-ATT-TTTA
1 -TTT-AAAATTTTTTAATTATTTA
1123340 TTTAAAATTTTTTAATTATTTA
1 TTTAAAATTTTTTAATTATTTA
1123362 TTTA
1 TTTA
1123366 TTCAATATGA
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
20 7 0.19
21 6 0.17
22 15 0.42
23 6 0.17
24 2 0.06
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.62
Consensus pattern (22 bp):
TTTAAAATTTTTTAATTATTTA
Found at i:1123482 original size:25 final size:26
Alignment explanation
Indices: 1123422--1123488 Score: 77
Period size: 25 Copynumber: 2.7 Consensus size: 26
1123412 ATATTTAAAT
*
1123422 AAATATAT-AAAATAATATATTTTTA
1 AAATATATAAAAATAATATATTATTA
*
1123447 AAA-ATTTTAAAAATAA-ATATTATTA
1 AAATA-TATAAAAATAATATATTATTA
*
1123472 AAATATATAAATATAAT
1 AAATATATAAAAATAAT
1123489 TCATTAATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
24 1 0.03
25 25 0.74
26 8 0.24
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (26 bp):
AAATATATAAAAATAATATATTATTA
Found at i:1123544 original size:6 final size:7
Alignment explanation
Indices: 1123523--1123548 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1123513 ATATTTAATA
1123523 TTTATTT
1 TTTATTT
1123530 TTTATTT
1 TTTATTT
1123537 TTTATTT
1 TTTATTT
1123544 TTTAT
1 TTTAT
1123549 CTTAGCATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTATTT
Found at i:1127067 original size:79 final size:79
Alignment explanation
Indices: 1126936--1127092 Score: 269
Period size: 79 Copynumber: 2.0 Consensus size: 79
1126926 CATAAGAGCT
* * *
1126936 AGTTTAATGAGTACTAGCAATGTGGCCATTGAGCACTATGAGCTCTTGTTGGAGTGGTAAAGATG
1 AGTTTAAGGAGTACTAGCAATGTGGACATTGAGCACGATGAGCTCTTGTTGGAGTGGTAAAGATG
1127001 TCATAGTTTTAAGA
66 TCATAGTTTTAAGA
* *
1127015 AGTTTAAGGATTACTAGCAATGTGGACATTGAGCACGATTAGCTCTTGTTGGAGTGGTAAAGATG
1 AGTTTAAGGAGTACTAGCAATGTGGACATTGAGCACGATGAGCTCTTGTTGGAGTGGTAAAGATG
1127080 TCATAGTTTTAAG
66 TCATAGTTTTAAG
1127093 GAGGAAATCA
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
79 73 1.00
ACGTcount: A:0.29, C:0.11, G:0.27, T:0.33
Consensus pattern (79 bp):
AGTTTAAGGAGTACTAGCAATGTGGACATTGAGCACGATGAGCTCTTGTTGGAGTGGTAAAGATG
TCATAGTTTTAAGA
Found at i:1131402 original size:40 final size:40
Alignment explanation
Indices: 1131347--1131426 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
1131337 ATATAGGCCA
1131347 AGTCTACAACCAATGCAGCATAGAATTTTACAATCACATT
1 AGTCTACAACCAATGCAGCATAGAATTTTACAATCACATT
* *
1131387 AGTCTACAACCAATGCAGGATAGAATTTTACAGTCACATT
1 AGTCTACAACCAATGCAGCATAGAATTTTACAATCACATT
1131427 TCTCTCAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.39, C:0.21, G:0.12, T:0.28
Consensus pattern (40 bp):
AGTCTACAACCAATGCAGCATAGAATTTTACAATCACATT
Found at i:1131620 original size:3 final size:3
Alignment explanation
Indices: 1131612--1131637 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1131602 AATTAGCCAT
1131612 ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG AT
1131638 CAAGAAAGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.31, T:0.35
Consensus pattern (3 bp):
ATG
Found at i:1136707 original size:24 final size:24
Alignment explanation
Indices: 1136660--1136707 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1136650 AACAATCTAC
*
1136660 AAGTTCAGCTCCTTCTTCAACTAT
1 AAGTTCAGCTCCTTCCTCAACTAT
* * *
1136684 AAGTTCAGTTCTTTCCTCACCTAT
1 AAGTTCAGCTCCTTCCTCAACTAT
1136708 TGATAACAAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.23, C:0.29, G:0.08, T:0.40
Consensus pattern (24 bp):
AAGTTCAGCTCCTTCCTCAACTAT
Found at i:1139661 original size:18 final size:19
Alignment explanation
Indices: 1139623--1139660 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1139613 AATCGATCTA
*
1139623 TTGAAAAAGTTGGTAATTT
1 TTGAAAAAGATGGTAATTT
1139642 TTGAAAAA-ATGGT-ATTT
1 TTGAAAAAGATGGTAATTT
1139659 TT
1 TT
1139661 TTTATAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 4 0.22
19 8 0.44
ACGTcount: A:0.37, C:0.00, G:0.18, T:0.45
Consensus pattern (19 bp):
TTGAAAAAGATGGTAATTT
Found at i:1148797 original size:18 final size:19
Alignment explanation
Indices: 1148776--1148817 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
1148766 TCTGTAAGTT
*
1148776 ATTAAAATT-AATATTTTA
1 ATTAAAATTAAAAATTTTA
*
1148794 ATT-AAATTAAAAATTTTG
1 ATTAAAATTAAAAATTTTA
1148812 ATTAAA
1 ATTAAA
1148818 CTCCTTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 5 0.25
18 13 0.65
19 2 0.10
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (19 bp):
ATTAAAATTAAAAATTTTA
Found at i:1151343 original size:13 final size:13
Alignment explanation
Indices: 1151325--1151404 Score: 61
Period size: 13 Copynumber: 5.4 Consensus size: 13
1151315 TTCAACAATT
1151325 TGTATCGATACAA
1 TGTATCGATACAA
1151338 TGTATCGATACATGA
1 TGTATCGATACA--A
*
1151353 GTGTTGTATCGATAAAA
1 ----TGTATCGATACAA
1151370 TGTATCGATACATAA
1 TGTATCGATAC--AA
1151385 GTTGTATCGATACAA
1 --TGTATCGATACAA
1151400 TGTAT
1 TGTAT
1151405 TGCTACGAAG
Statistics
Matches: 55, Mismatches: 2, Indels: 20
0.71 0.03 0.26
Matches are distributed among these distances:
13 27 0.49
15 5 0.09
17 12 0.22
19 11 0.20
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1151365 original size:32 final size:30
Alignment explanation
Indices: 1151324--1151404 Score: 126
Period size: 32 Copynumber: 2.6 Consensus size: 30
1151314 TTTCAACAAT
*
1151324 TTGTATCGATACAATGTATCGATACATGAGTG
1 TTGTATCGATACAATGTATCGATACAT-A-AG
*
1151356 TTGTATCGATAAAATGTATCGATACATAAG
1 TTGTATCGATACAATGTATCGATACATAAG
1151386 TTGTATCGATACAATGTAT
1 TTGTATCGATACAATGTAT
1151405 TGCTACGAAG
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
30 19 0.41
31 1 0.02
32 26 0.57
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.36
Consensus pattern (30 bp):
TTGTATCGATACAATGTATCGATACATAAG
Found at i:1151390 original size:17 final size:17
Alignment explanation
Indices: 1151338--1151398 Score: 67
Period size: 17 Copynumber: 3.7 Consensus size: 17
1151328 ATCGATACAA
*
1151338 TGTATCGATACATGAGTGT
1 TGTATCGATACAT-A-AGT
1151357 TGTATCGATA-A-AA--
1 TGTATCGATACATAAGT
1151370 TGTATCGATACATAAGT
1 TGTATCGATACATAAGT
1151387 TGTATCGATACA
1 TGTATCGATACA
1151399 ATGTATTGCT
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
13 10 0.27
14 1 0.03
15 2 0.05
16 1 0.03
17 12 0.32
18 1 0.03
19 10 0.27
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.34
Consensus pattern (17 bp):
TGTATCGATACATAAGT
Found at i:1151528 original size:52 final size:52
Alignment explanation
Indices: 1151445--1151547 Score: 145
Period size: 52 Copynumber: 2.0 Consensus size: 52
1151435 CGATACATTA
***
1151445 CCCAAATGTATCGATACACTGATCTTTGTATCGATACATACAGGCAAATTTG
1 CCCAAATGTATCGATACACTGATAAATGTATCGATACATACAGGCAAATTTG
* *
1151497 CCCAGATGTATCGATACACT-ATGAAATGTATCGATACATGCAGGCAAATTT
1 CCCAAATGTATCGATACACTGAT-AAATGTATCGATACATACAGGCAAATTT
1151548 TCAAATTTCG
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
51 2 0.04
52 43 0.96
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (52 bp):
CCCAAATGTATCGATACACTGATAAATGTATCGATACATACAGGCAAATTTG
Found at i:1154956 original size:11 final size:10
Alignment explanation
Indices: 1154940--1154972 Score: 50
Period size: 11 Copynumber: 3.3 Consensus size: 10
1154930 AGCAAAGTAA
1154940 ATAATTATTT
1 ATAATTATTT
1154950 GATAATTATTT
1 -ATAATTATTT
1154961 ATAA-TATTT
1 ATAATTATTT
1154970 ATA
1 ATA
1154973 TGAAGTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 8 0.36
10 4 0.18
11 10 0.45
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (10 bp):
ATAATTATTT
Found at i:1156939 original size:32 final size:32
Alignment explanation
Indices: 1156880--1156940 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
1156870 TTCATACAAA
* **
1156880 TGCTTTGGGTAAAGGTAAATATGATTCAAGTT
1 TGCTTTGGGTAAAGGTAAACAAAATTCAAGTT
* *
1156912 TGCTTTGGGTAGAGGTAACCAAAATTCAA
1 TGCTTTGGGTAAAGGTAAACAAAATTCAA
1156941 TTCTTGAATG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 24 1.00
ACGTcount: A:0.33, C:0.10, G:0.25, T:0.33
Consensus pattern (32 bp):
TGCTTTGGGTAAAGGTAAACAAAATTCAAGTT
Found at i:1157750 original size:21 final size:21
Alignment explanation
Indices: 1157711--1157750 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1157701 GAAATATGCA
*
1157711 TTGTATCAATATAAGGTCAGG
1 TTGTATCAATACAAGGTCAGG
*
1157732 TTGTATCAATACAATGTCA
1 TTGTATCAATACAAGGTCA
1157751 AGTATTGTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.35
Consensus pattern (21 bp):
TTGTATCAATACAAGGTCAGG
Found at i:1158969 original size:2 final size:2
Alignment explanation
Indices: 1158962--1159003 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1158952 TGATGTTTAG
1158962 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1159004 TTAGGAATGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1159308 original size:45 final size:45
Alignment explanation
Indices: 1159249--1159341 Score: 118
Period size: 45 Copynumber: 2.1 Consensus size: 45
1159239 ATGTTAGTGT
* * *
1159249 TATTTAGGTCA-TTTTCAATGATCT-AGGAATTTTATGCAAATTTCA
1 TATTTAGGTAATTTTTC-ATCATCTAAGG-ACTTTATGCAAATTTCA
*
1159294 TATTTGGGTAATTTTTCATCATCTAAGGACTTTATGCAAATTTCA
1 TATTTAGGTAATTTTTCATCATCTAAGGACTTTATGCAAATTTCA
1159339 TAT
1 TAT
1159342 ATTTTGATAT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
45 34 0.81
46 8 0.19
ACGTcount: A:0.30, C:0.12, G:0.13, T:0.45
Consensus pattern (45 bp):
TATTTAGGTAATTTTTCATCATCTAAGGACTTTATGCAAATTTCA
Found at i:1159379 original size:58 final size:57
Alignment explanation
Indices: 1159295--1159475 Score: 166
Period size: 58 Copynumber: 3.1 Consensus size: 57
1159285 CAAATTTCAT
* * * *
1159295 ATTTGGGTAATTTTTCATCATCTAAGGACTTTATGCAAATTTCAT-ATATTTTGATATC
1 ATTTAGGTAATTTTCCATGATTTAAGGACTTTATG-AAATTTCATGA-ATTTTGATATC
* * *
1159353 ATTTAGGTAATTTTCCATGATTTAAGGACTTTGATGTAATTTTATGAATTTTGATGTC
1 ATTTAGGTAATTTTCCATGATTTAAGGACTTT-ATGAAATTTCATGAATTTTGATATC
** * * * * * * * *
1159411 ATTTACATCATTTTCTATGATTTAGGGATTTTAGTGTAACTTCTTGAATTTTGATGTC
1 ATTTAGGTAATTTTCCATGATTTAAGGACTTTA-TGAAATTTCATGAATTTTGATATC
1159469 ATTTAGG
1 ATTTAGG
1159476 CCATTTTTCT
Statistics
Matches: 102, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
57 1 0.01
58 97 0.95
59 4 0.04
ACGTcount: A:0.27, C:0.09, G:0.15, T:0.48
Consensus pattern (57 bp):
ATTTAGGTAATTTTCCATGATTTAAGGACTTTATGAAATTTCATGAATTTTGATATC
Found at i:1159520 original size:58 final size:58
Alignment explanation
Indices: 1159317--1159513 Score: 186
Period size: 58 Copynumber: 3.4 Consensus size: 58
1159307 TTTCATCATC
* * * * *
1159317 TAAGGACTTT-ATGCAAATTTCAT-ATATTTTGATATCATTTAGGTAATTTTCCATGATT
1 TAAGGACTTTGATG-TAATTTCATGA-ATTTTGATGTCATTTAGGTCATTTTTCTTGATT
* **
1159375 TAAGGACTTTGATGTAATTTTATGAATTTTGATGTCATTTACATCA-TTTTCTATGATT
1 TAAGGACTTTGATGTAATTTCATGAATTTTGATGTCATTTAGGTCATTTTTCT-TGATT
* * * * * *
1159433 TAGGGA-TTTTAGTGTAACTTCTTGAATTTTGATGTCATTTAGGCCATTTTTCTTGATC
1 TAAGGACTTTGA-TGTAATTTCATGAATTTTGATGTCATTTAGGTCATTTTTCTTGATT
* *
1159491 TAAGAACTTCGATGTAATTTCAT
1 TAAGGACTTTGATGTAATTTCAT
1159514 ATATTTTAGA
Statistics
Matches: 110, Mismatches: 23, Indels: 12
0.76 0.16 0.08
Matches are distributed among these distances:
57 8 0.07
58 89 0.81
59 13 0.12
ACGTcount: A:0.27, C:0.11, G:0.15, T:0.47
Consensus pattern (58 bp):
TAAGGACTTTGATGTAATTTCATGAATTTTGATGTCATTTAGGTCATTTTTCTTGATT
Found at i:1159978 original size:11 final size:11
Alignment explanation
Indices: 1159964--1159993 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1159954 TTTAAAATTC
1159964 ATTTAAATCCA
1 ATTTAAATCCA
1159975 ATTTAAATCCA
1 ATTTAAATCCA
*
1159986 ATTCAAAT
1 ATTTAAAT
1159994 ATGGGAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.47, C:0.17, G:0.00, T:0.37
Consensus pattern (11 bp):
ATTTAAATCCA
Found at i:1160649 original size:20 final size:22
Alignment explanation
Indices: 1160610--1160650 Score: 59
Period size: 20 Copynumber: 1.9 Consensus size: 22
1160600 TTTTTCTTTG
1160610 ATTTTTCATTTCTTTTTGCTATA
1 ATTTTTCATTTC-TTTTGCTATA
1160633 ATTTTTC-TTTC-TTTGCTA
1 ATTTTTCATTTCTTTTGCTA
1160651 AAACGCATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
22 4 0.22
23 7 0.39
ACGTcount: A:0.15, C:0.15, G:0.05, T:0.66
Consensus pattern (22 bp):
ATTTTTCATTTCTTTTGCTATA
Found at i:1161673 original size:33 final size:32
Alignment explanation
Indices: 1161613--1161676 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
1161603 TATTTTAGTG
* *
1161613 TGTATCGATACAATGAACATGTATCGATACAA
1 TGTATCGATAAAAAGAACATGTATCGATACAA
*
1161645 TGTATCGATAAAAAGCAATATGTATCGATACA
1 TGTATCGATAAAAAG-AACATGTATCGATACA
1161677 TTTGGGTGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 13 0.46
33 15 0.54
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (32 bp):
TGTATCGATAAAAAGAACATGTATCGATACAA
Found at i:1161803 original size:21 final size:21
Alignment explanation
Indices: 1161778--1161817 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1161768 TTTGGATTAT
*
1161778 TTTTTA-CTTGAAAACATATGA
1 TTTTTATCTT-AAAAAATATGA
1161799 TTTTTATCTTAAAAAATAT
1 TTTTTATCTTAAAAAATAT
1161818 TTATACTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.47
Consensus pattern (21 bp):
TTTTTATCTTAAAAAATATGA
Found at i:1162325 original size:21 final size:23
Alignment explanation
Indices: 1162296--1162337 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
1162286 CAATATATAA
*
1162296 CTCCTCTTAATAAAAT-TTTTCT
1 CTCCTCTTAACAAAATATTTTCT
1162318 CTCC-CTTAACAAAATATTTT
1 CTCCTCTTAACAAAATATTTT
1162338 ATGCTTTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.31, C:0.24, G:0.00, T:0.45
Consensus pattern (23 bp):
CTCCTCTTAACAAAATATTTTCT
Found at i:1162672 original size:10 final size:9
Alignment explanation
Indices: 1162637--1162684 Score: 55
Period size: 10 Copynumber: 5.2 Consensus size: 9
1162627 AAAGCATATT
1162637 CATAAATAA
1 CATAAATAA
1162646 CATAAAGTCAA
1 CATAAA-T-AA
1162657 CATAAATAA
1 CATAAATAA
1162666 GCATAAATAA
1 -CATAAATAA
1162676 -ATAAA-AA
1 CATAAATAA
1162683 CA
1 CA
1162685 ACTACTCCTA
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
7 2 0.06
8 6 0.17
9 8 0.23
10 11 0.31
11 8 0.23
ACGTcount: A:0.65, C:0.12, G:0.04, T:0.19
Consensus pattern (9 bp):
CATAAATAA
Found at i:1163667 original size:17 final size:17
Alignment explanation
Indices: 1163645--1163680 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1163635 TTTGGTTATA
1163645 GTGTTTGACATTTGCTT
1 GTGTTTGACATTTGCTT
* *
1163662 GTGTTTGAGATTTTCTT
1 GTGTTTGACATTTGCTT
1163679 GT
1 GT
1163681 CTTCGGAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.11, C:0.08, G:0.25, T:0.56
Consensus pattern (17 bp):
GTGTTTGACATTTGCTT
Found at i:1168893 original size:3 final size:3
Alignment explanation
Indices: 1168885--1168922 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
1168875 AACCTCTTCC
*
1168885 TCA TCA TCA TCA TTA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
1168923 TTTATCATCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.37
Consensus pattern (3 bp):
TCA
Found at i:1168935 original size:9 final size:9
Alignment explanation
Indices: 1168885--1168931 Score: 58
Period size: 9 Copynumber: 5.2 Consensus size: 9
1168875 AACCTCTTCC
*
1168885 TCATCATCA
1 TCATTATCA
1168894 TCATTATCA
1 TCATTATCA
*
1168903 TCATCATCA
1 TCATTATCA
*
1168912 TCATCATCA
1 TCATTATCA
*
1168921 TCTTTATCA
1 TCATTATCA
1168930 TC
1 TC
1168932 TTTAATGGTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 34 1.00
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.40
Consensus pattern (9 bp):
TCATTATCA
Found at i:1170248 original size:13 final size:13
Alignment explanation
Indices: 1170230--1170264 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
1170220 AATGAGCTTT
1170230 CAAAGAATAATAA
1 CAAAGAATAATAA
1170243 CAAAGAATAATAA
1 CAAAGAATAATAA
1170256 CAAAGAATA
1 CAAAGAATA
1170265 CAAAAGCTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.69, C:0.09, G:0.09, T:0.14
Consensus pattern (13 bp):
CAAAGAATAATAA
Found at i:1171209 original size:20 final size:19
Alignment explanation
Indices: 1171163--1171216 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
1171153 TTTTGGACCA
*
1171163 TAATGTATTGGTACATGGC
1 TAATGTATTGATACATGGC
* *
1171182 CATTTGTATTGATACATAGGC
1 TA-ATGTATTGATACAT-GGC
1171203 TAATGTATTGATAC
1 TAATGTATTGATAC
1171217 TTTTTGGCTA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 1 0.04
20 23 0.82
21 4 0.14
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.39
Consensus pattern (19 bp):
TAATGTATTGATACATGGC
Found at i:1171244 original size:20 final size:21
Alignment explanation
Indices: 1171186--1171258 Score: 69
Period size: 20 Copynumber: 3.4 Consensus size: 21
1171176 CATGGCCATT
*
1171186 TGTATTGATACA-TAGGCTAA
1 TGTATTGATACATTTGGCTAA
*
1171206 TGTATTGATACTTTTTGGCT-A
1 TGTATTGATAC-ATTTGGCTAA
*
1171227 TGTATCGATACATTTGGCCTAA
1 TGTATTGATACATTTGG-CTAA
*
1171249 TTATATTGAT
1 -TGTATTGAT
1171259 GTATCCTCAA
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
20 16 0.38
21 13 0.31
22 6 0.14
23 7 0.17
ACGTcount: A:0.27, C:0.11, G:0.18, T:0.44
Consensus pattern (21 bp):
TGTATTGATACATTTGGCTAA
Found at i:1187715 original size:21 final size:20
Alignment explanation
Indices: 1187691--1187733 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1187681 TCTTACTATC
*
1187691 ATAATATTTAATTTTATAATT
1 ATAATAATTAA-TTTATAATT
*
1187712 ATAATAATTAATTTATTATT
1 ATAATAATTAATTTATAATT
1187732 AT
1 AT
1187734 TATTATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
ATAATAATTAATTTATAATT
Found at i:1187733 original size:26 final size:26
Alignment explanation
Indices: 1187696--1187751 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
1187686 CTATCATAAT
1187696 ATTTAATTTTATAATTATAATAATTA
1 ATTTAATTTTATAATTATAATAATTA
* * *
1187722 ATTT-ATTATTATTATTATTATTATTA
1 ATTTAATT-TTATAATTATAATAATTA
1187748 ATTT
1 ATTT
1187752 TTTAAAAATC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 3 0.12
26 23 0.88
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (26 bp):
ATTTAATTTTATAATTATAATAATTA
Found at i:1191222 original size:7 final size:7
Alignment explanation
Indices: 1191212--1191251 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
1191202 AATATATTTT
1191212 TTATTAA
1 TTATTAA
1191219 TTATTAA
1 TTATTAA
1191226 TTATTAA
1 TTATTAA
1191233 TTATTAA
1 TTATTAA
* *
1191240 TTTTTTA
1 TTATTAA
1191247 TTATT
1 TTATT
1191252 TTTACTCAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (7 bp):
TTATTAA
Found at i:1191525 original size:18 final size:17
Alignment explanation
Indices: 1191490--1191529 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
1191480 GAAACTAGTT
1191490 AAAAAAATAAAAAAATA
1 AAAAAAATAAAAAAATA
* *
1191507 AAAAAAATCAAACATATA
1 AAAAAAAT-AAAAAAATA
1191525 AAAAA
1 AAAAA
1191530 TACATTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.82, C:0.05, G:0.00, T:0.12
Consensus pattern (17 bp):
AAAAAAATAAAAAAATA
Found at i:1195226 original size:21 final size:22
Alignment explanation
Indices: 1195202--1195245 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
1195192 AAATTATAAA
* *
1195202 TATTTAAATTTATAT-TTAATT
1 TATTGAAAGTTATATCTTAATT
*
1195223 TATTGAACGTTATATCTTAATT
1 TATTGAAAGTTATATCTTAATT
1195245 T
1 T
1195246 TTCACTTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.57
Consensus pattern (22 bp):
TATTGAAAGTTATATCTTAATT
Found at i:1196869 original size:21 final size:21
Alignment explanation
Indices: 1196840--1196932 Score: 73
Period size: 21 Copynumber: 4.4 Consensus size: 21
1196830 TTGCCAAAAT
* *
1196840 ACAAATTACCTATACTCATAA
1 ACAAGTTACCTATACTAATAA
*
1196861 ACAAGTTACCTATGCTAATAA
1 ACAAGTTACCTATACTAATAA
* * *
1196882 ACAAGTTA--TTTAGGTCAATAG
1 ACAAGTTACCTATA-CT-AATAA
* *
1196903 ACAAGTTACTTATACCAATAA
1 ACAAGTTACCTATACTAATAA
*
1196924 ACGAGTTAC
1 ACAAGTTAC
1196933 ATGTTTCGAT
Statistics
Matches: 56, Mismatches: 12, Indels: 8
0.74 0.16 0.11
Matches are distributed among these distances:
19 2 0.04
20 1 0.02
21 50 0.89
23 3 0.05
ACGTcount: A:0.43, C:0.18, G:0.10, T:0.29
Consensus pattern (21 bp):
ACAAGTTACCTATACTAATAA
Found at i:1198282 original size:17 final size:16
Alignment explanation
Indices: 1198253--1198286 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1198243 CGGGCTCAGA
1198253 TTTTTTTGATTCAAGC
1 TTTTTTTGATTCAAGC
*
1198269 TTTTTTGTGGTTCAAGC
1 TTTTTT-TGATTCAAGC
1198286 T
1 T
1198287 ATCTTAGGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.12, G:0.18, T:0.56
Consensus pattern (16 bp):
TTTTTTTGATTCAAGC
Found at i:1206518 original size:15 final size:14
Alignment explanation
Indices: 1206498--1206527 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
1206488 TATATAAATT
1206498 TTAATAAATTAATAA
1 TTAATAAATT-ATAA
1206513 TTAATAAATTATAA
1 TTAATAAATTATAA
1206527 T
1 T
1206528 ATATTTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAATAAATTATAA
Found at i:1206539 original size:10 final size:10
Alignment explanation
Indices: 1206521--1206553 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
1206511 AATTAATAAA
1206521 TTATAATATAT
1 TTAT-ATATAT
1206532 TTATATATAT
1 TTATATATAT
1206542 TTATA-ATAT
1 TTATATATAT
1206551 TTA
1 TTA
1206554 ATTTAATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 7 0.32
10 11 0.50
11 4 0.18
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (10 bp):
TTATATATAT
Found at i:1206562 original size:19 final size:21
Alignment explanation
Indices: 1206507--1206555 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 21
1206497 TTTAATAAAT
1206507 TAATA-ATTAATA-A-A-TTA
1 TAATATATTAATATATATTTA
*
1206524 TAATATATTTATATATATTTA
1 TAATATATTAATATATATTTA
1206545 TAATAT-TTAAT
1 TAATATATTAAT
1206556 TTAATTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 5 0.19
18 6 0.23
19 1 0.04
20 5 0.19
21 9 0.35
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TAATATATTAATATATATTTA
Found at i:1206925 original size:25 final size:25
Alignment explanation
Indices: 1206874--1206930 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
1206864 TTATTCCTTC
*
1206874 AAATGAATAATTATTCAGGAAAAATT
1 AAAT-AATAATTATTCAGAAAAAATT
*
1206900 AAATAATTATTATTCA-AAAAATATT
1 AAATAATAATTATTCAGAAAAA-ATT
*
1206925 ATATAA
1 AAATAA
1206931 AATATTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 4 0.15
25 19 0.70
26 4 0.15
ACGTcount: A:0.56, C:0.04, G:0.05, T:0.35
Consensus pattern (25 bp):
AAATAATAATTATTCAGAAAAAATT
Found at i:1208093 original size:2 final size:2
Alignment explanation
Indices: 1208088--1208122 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1208078 TTTTAAATTT
1208088 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1208123 CATCTATCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1208132 original size:7 final size:7
Alignment explanation
Indices: 1208120--1208165 Score: 65
Period size: 7 Copynumber: 6.4 Consensus size: 7
1208110 TATATATATA
1208120 TATCATC
1 TATCATC
1208127 TATCATC
1 TATCATC
1208134 TATCATC
1 TATCATC
1208141 TATCATC
1 TATCATC
* *
1208148 GATTATC
1 TATCATC
1208155 TATCTATC
1 TATC-ATC
1208163 TAT
1 TAT
1208166 TTATATATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
7 28 0.82
8 6 0.18
ACGTcount: A:0.28, C:0.24, G:0.02, T:0.46
Consensus pattern (7 bp):
TATCATC
Found at i:1217546 original size:51 final size:51
Alignment explanation
Indices: 1217490--1217624 Score: 171
Period size: 51 Copynumber: 2.6 Consensus size: 51
1217480 TGCCTCCATG
* * * * *
1217490 TATCGATACATTAAAGAATATATCAATACATTTAGGTCAAAACCAAGAATA
1 TATCGATATAATAAAGAATGTATCGATACATTTAGGTAAAAACCAAGAATA
* * ** *
1217541 TATCGATATAATGAAGAATGTATCGATACATTTGGGTAAAAACCCTGAATG
1 TATCGATATAATAAAGAATGTATCGATACATTTAGGTAAAAACCAAGAATA
*
1217592 TATCGATATAATAAAAAATGTATCGATACATTT
1 TATCGATATAATAAAGAATGTATCGATACATTT
1217625 TCATTCCAAA
Statistics
Matches: 72, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 72 1.00
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.30
Consensus pattern (51 bp):
TATCGATATAATAAAGAATGTATCGATACATTTAGGTAAAAACCAAGAATA
Found at i:1222007 original size:13 final size:14
Alignment explanation
Indices: 1221979--1222008 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1221969 TAAATTGAGG
1221979 CAGAAAGTGCTTTT
1 CAGAAAGTGCTTTT
1221993 CAGAAAGTG-TTTT
1 CAGAAAGTGCTTTT
1222006 CAG
1 CAG
1222009 CAATTTATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.33
Consensus pattern (14 bp):
CAGAAAGTGCTTTT
Found at i:1224852 original size:22 final size:22
Alignment explanation
Indices: 1224820--1224861 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1224810 TGAGAAAGTC
1224820 TAAATACAAAA-ATAATATAATG
1 TAAATACAAAACAT-ATATAATG
*
1224842 TAAATATAAAACATATATAA
1 TAAATACAAAACATATATAA
1224862 AAAATTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.29
Consensus pattern (22 bp):
TAAATACAAAACATATATAATG
Found at i:1225028 original size:2 final size:2
Alignment explanation
Indices: 1225021--1225051 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1225011 TCAAATATTC
1225021 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1225052 ACTTCAGTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1229846 original size:24 final size:20
Alignment explanation
Indices: 1229798--1229897 Score: 69
Period size: 20 Copynumber: 4.8 Consensus size: 20
1229788 ATCGTGTGTC
*
1229798 AATGTATCGATACAATTTGG
1 AATGTATCGATACAATTTGA
1229818 AATGTATCGATACATGCATTTGAA
1 AATGTATCGATACA---ATTTG-A
* * **
1229842 AATGTAGCCGTTACAAACT--
1 AATGTA-TCGATACAATTTGA
1229861 AATGTATCGATACAATTTGA
1 AATGTATCGATACAATTTGA
* *
1229881 TCATGTAGCGATACAAT
1 -AATGTATCGATACAAT
1229898 GTATCGATAC
Statistics
Matches: 61, Mismatches: 11, Indels: 15
0.70 0.13 0.17
Matches are distributed among these distances:
18 8 0.13
19 6 0.10
20 14 0.23
21 14 0.23
22 2 0.03
23 5 0.08
24 6 0.10
25 6 0.10
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (20 bp):
AATGTATCGATACAATTTGA
Found at i:1229904 original size:34 final size:32
Alignment explanation
Indices: 1229861--1229928 Score: 93
Period size: 34 Copynumber: 2.1 Consensus size: 32
1229851 GTTACAAACT
1229861 AATGTATCGATACAAT-TTGATCATGTAGCGATAC
1 AATGTATCGATAC-ATCTTG-T-ATGTAGCGATAC
*
1229895 AATGTATCGATACATCTTGTATGTATCGATAC
1 AATGTATCGATACATCTTGTATGTAGCGATAC
1229927 AA
1 AA
1229929 ACAGTTAAGG
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
32 13 0.41
33 3 0.09
34 16 0.50
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (32 bp):
AATGTATCGATACATCTTGTATGTAGCGATAC
Found at i:1229905 original size:13 final size:13
Alignment explanation
Indices: 1229861--1229908 Score: 52
Period size: 13 Copynumber: 4.1 Consensus size: 13
1229851 GTTACAAACT
1229861 AATGTATCGATAC
1 AATGTATCGATAC
1229874 AAT-T-T-GAT-C
1 AATGTATCGATAC
*
1229883 -ATGTAGCGATAC
1 AATGTATCGATAC
1229895 AATGTATCGATAC
1 AATGTATCGATAC
1229908 A
1 A
1229909 TCTTGTATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 10
0.70 0.05 0.25
Matches are distributed among these distances:
8 2 0.07
9 2 0.07
10 3 0.11
11 4 0.14
12 2 0.07
13 15 0.54
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.31
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:1230026 original size:13 final size:13
Alignment explanation
Indices: 1230008--1230033 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1229998 TACAGTAGTC
1230008 ATGTATCGATACA
1 ATGTATCGATACA
1230021 ATGTATCGATACA
1 ATGTATCGATACA
1230034 TCTGAAGGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1230875 original size:41 final size:42
Alignment explanation
Indices: 1230798--1230882 Score: 104
Period size: 41 Copynumber: 2.0 Consensus size: 42
1230788 GCATTTTTTT
* *
1230798 TAAAAATAAAAATATTATTTTTATTTAATTTTTATTAAAATA
1 TAAAAATAAAAATATTATTTTTATATAATTTATATTAAAATA
*
1230840 TAAAATATAAATAATA-TATTTTTA-AT-ATTTATATTATAATA
1 TAAAA-ATAAA-AATATTATTTTTATATAATTTATATTAAAATA
1230881 TA
1 TA
1230883 GTATATTTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
41 15 0.39
42 6 0.16
43 13 0.34
44 4 0.11
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (42 bp):
TAAAAATAAAAATATTATTTTTATATAATTTATATTAAAATA
Found at i:1231132 original size:21 final size:21
Alignment explanation
Indices: 1231106--1231148 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1231096 TAAAAATTAT
*
1231106 TTTTAT-ATTAATATTTATATA
1 TTTTATAATTAAT-TTTAAATA
1231127 TTTTATAATTAATTTTAAATA
1 TTTTATAATTAATTTTAAATA
1231148 T
1 T
1231149 AAATATATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTTATAATTAATTTTAAATA
Found at i:1231853 original size:20 final size:21
Alignment explanation
Indices: 1231817--1231855 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1231807 CATCATTTAA
*
1231817 ATTTAAAAAAGATATATATTG
1 ATTTAAAAAAGAAATATATTG
1231838 ATTTAAAAAA-AAATATAT
1 ATTTAAAAAAGAAATATAT
1231856 GTTAATTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (21 bp):
ATTTAAAAAAGAAATATATTG
Found at i:1231867 original size:22 final size:22
Alignment explanation
Indices: 1231821--1231868 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
1231811 ATTTAAATTT
* * *
1231821 AAAAAAGATATATATTGATTTA
1 AAAAAAAATATATATTAATTGA
*
1231843 AAAAAAAATATATGTTAATTGA
1 AAAAAAAATATATATTAATTGA
1231865 AAAA
1 AAAA
1231869 TTATTTCATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.31
Consensus pattern (22 bp):
AAAAAAAATATATATTAATTGA
Found at i:1234532 original size:15 final size:15
Alignment explanation
Indices: 1234512--1234541 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1234502 ATATGGCTTT
1234512 GCTTTTTTTTTTTAG
1 GCTTTTTTTTTTTAG
1234527 GCTTTTTTTTTTTAG
1 GCTTTTTTTTTTTAG
1234542 AAAGTTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.07, C:0.07, G:0.13, T:0.73
Consensus pattern (15 bp):
GCTTTTTTTTTTTAG
Found at i:1238101 original size:18 final size:19
Alignment explanation
Indices: 1238062--1238108 Score: 69
Period size: 18 Copynumber: 2.5 Consensus size: 19
1238052 TTTAATATTT
*
1238062 ACTGCTACTTAAGAAAACA
1 ACTGCTACTTAAGAAAAAA
1238081 ACTGCTACTTAA-AAAAAA
1 ACTGCTACTTAAGAAAAAA
*
1238099 ACTACTACTT
1 ACTGCTACTT
1238109 GAATAGCTCG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 14 0.54
19 12 0.46
ACGTcount: A:0.47, C:0.21, G:0.06, T:0.26
Consensus pattern (19 bp):
ACTGCTACTTAAGAAAAAA
Found at i:1239872 original size:30 final size:28
Alignment explanation
Indices: 1239838--1239893 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 28
1239828 TCAATGATTA
1239838 GAAAATAAATCGAGATTGGAGTATCCCCTC
1 GAAAAT-AA-CGAGATTGGAGTATCCCCTC
*
1239868 GAAAATAACGGGATTGGAGTATCCCC
1 GAAAATAACGAGATTGGAGTATCCCC
1239894 AATTACGAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 17 0.68
29 2 0.08
30 6 0.24
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.21
Consensus pattern (28 bp):
GAAAATAACGAGATTGGAGTATCCCCTC
Found at i:1239889 original size:78 final size:79
Alignment explanation
Indices: 1239804--1239975 Score: 204
Period size: 79 Copynumber: 2.2 Consensus size: 79
1239794 ACAACAGGGC
* ** *
1239804 TGGAGTATCCCCGGTTGTGAGAAATCAATGA-TTAGAAAATAAA-TCGAGATTGGAGTATCCCCT
1 TGGAGTATCCCCGATTACGAGAAATCAAT-ATTTAGAAAATAAAGCCGAGATTGGAGTATCCCCT
1239867 CGAAAATAACGGGAT
65 CGAAAATAACGGGAT
* * ** * *
1239882 TGGAGTATCCCCAATTACGAGAAATCAATATTTTGGGAATAAAGCCGGGGTTGGAGTATCCCCTC
1 TGGAGTATCCCCGATTACGAGAAATCAATATTTAGAAAATAAAGCCGAGATTGGAGTATCCCCTC
* * *
1239947 GGAAGTAACGGGGT
66 GAAAATAACGGGAT
1239961 TGGAGTATCCCCGAT
1 TGGAGTATCCCCGAT
1239976 GAAATAACGA
Statistics
Matches: 78, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
77 1 0.01
78 34 0.44
79 43 0.55
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.24
Consensus pattern (79 bp):
TGGAGTATCCCCGATTACGAGAAATCAATATTTAGAAAATAAAGCCGAGATTGGAGTATCCCCTC
GAAAATAACGGGAT
Found at i:1239967 original size:28 final size:28
Alignment explanation
Indices: 1239927--1239998 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
1239917 GGAATAAAGC
** *
1239927 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
1239955 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
1239983 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
1239999 TCGATTATGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:1240172 original size:159 final size:155
Alignment explanation
Indices: 1239987--1240373 Score: 383
Period size: 159 Copynumber: 2.4 Consensus size: 155
1239977 AAATAACGAG
* * *
1239987 GTTGGAGTATCCTCGATTATGAAAAATTGGTATTTTTTTGGAAATAAAATCGGAGTTGGAGTATC
1 GTTGGAGTATCCCCGATTATGAAAAA-T--TAATATTTTGGAAATAAAATCGGAGTTGGAGTATC
* **
1240052 CCCGATTAAAGGGAAAATTGGTGT-T-TTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTGTG
63 CCCGATTAAAGGG---ATTGGAGTATCCCGAAAAT-AAA-CGGGGTTGGAGTATCCCCGATTGT-
*
1240115 GAA-AAATT-A-GTGTTTTAGCAATAAAACCGG-
122 GAAGAAATTGATGTGTTTTAGAAATAAAACCGGA
* * * *
1240145 GATTGGAGTATCCCCGATTATGAAAAATCAATATTTTGGAGATAAAGTCGGGGTTGGAGTATCCC
1 G-TTGGAGTATCCCCGATTATGAAAAATTAATATTTTGGAAATAAAATCGGAGTTGGAGTAT-CC
* * * * *
1240210 CTCGAAAATAACGGGGTTGGAGTATCCCGATAATTAACGGGGTTGGAGTATCCCCGATTGTGAAG
64 C-CG--ATTAAAGGGATTGGAGTATCCCGAAAATAAACGGGGTTGGAGTATCCCCGATTGTGAAG
* * *
1240275 AAATTGATGTTTTTTGGAAATAAAATCGGA
126 AAATTGATGTGTTTTAGAAATAAAACCGGA
* * * *
1240305 GTTGGAGTATCCCCGATTAT-AGAAAATTAGTGTTTTGAAAATAAAATCGGAGTTGGAATATCCC
1 GTTGGAGTATCCCCGATTATGA-AAAATTAATATTTTGGAAATAAAATCGGAGTTGGAGTATCCC
1240369 CGATT
65 CGATT
1240374 GTGGAGAATT
Statistics
Matches: 189, Mismatches: 28, Indels: 27
0.77 0.11 0.11
Matches are distributed among these distances:
155 2 0.01
156 31 0.16
157 40 0.21
158 12 0.06
159 96 0.51
160 8 0.04
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.30
Consensus pattern (155 bp):
GTTGGAGTATCCCCGATTATGAAAAATTAATATTTTGGAAATAAAATCGGAGTTGGAGTATCCCC
GATTAAAGGGATTGGAGTATCCCGAAAATAAACGGGGTTGGAGTATCCCCGATTGTGAAGAAATT
GATGTGTTTTAGAAATAAAACCGGA
Found at i:1240202 original size:51 final size:51
Alignment explanation
Indices: 1239986--1240373 Score: 262
Period size: 51 Copynumber: 7.4 Consensus size: 51
1239976 GAAATAACGA
* * * *
1239986 GGTTGGAGTATCCTCGATTATGAAAAATTGGTATTTTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAA-T--TAGTGTTTTGGAAATAAAACCGG
* * * * *
1240040 AGTTGGAGTATCCCCGATTAAAGGGAAAATTGGTGTTTTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT--ATGAAAAATTAGTGTTTTGGAAATAAAACCGG
* * *
1240093 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGG
1 GGTTGGAGTATCCCCGATTAT-GAAAAATTAGTGTTTTGGAAATAAAACCGG
* * * * * **
1240145 GATTGGAGTATCCCCGATTATGAAAAATCAATATTTTGGAGATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGGAAATAAAACCGG
** *** * * *** *
1240196 GGTTGGAGTATCCCCTCGAAAAT-AACGGGGTTGGAGTATCCCGATAAT-TAA-CGG
1 GGTTGGAGTAT-CCC-CGATTATGAA--AAATTAGTGT-TTTGGA-AATAAAACCGG
* * *
1240250 GGTTGGAGTATCCCCGATTGTGAAGAAATTGATGTTTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAA-AAATT-A-GTGTTTTGGAAATAAAACCGG
* * *
1240304 AGTTGGAGTATCCCCGATTAT-AGAAAATTAGTGTTTTGAAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGA-AAAATTAGTGTTTTGGAAATAAAACCGG
* *
1240355 AGTTGGAATATCCCCGATT
1 GGTTGGAGTATCCCCGATT
1240374 GTGGAGAATT
Statistics
Matches: 257, Mismatches: 62, Indels: 33
0.73 0.18 0.09
Matches are distributed among these distances:
51 69 0.27
52 60 0.23
53 57 0.22
54 58 0.23
55 5 0.02
56 8 0.03
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGGAAATAAAACCGG
Found at i:1240233 original size:28 final size:28
Alignment explanation
Indices: 1240193--1240264 Score: 105
Period size: 26 Copynumber: 2.6 Consensus size: 28
1240183 GAGATAAAGT
1240193 CGGGGTTGGAGTATCCCCTCGA-AAATAA
1 CGGGGTTGGAGTATCCCC-CGATAAATAA
*
1240221 CGGGGTTGGAGTAT--CCCGATAATTAA
1 CGGGGTTGGAGTATCCCCCGATAAATAA
1240247 CGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
1240265 GATTGTGAAG
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
25 3 0.08
26 21 0.52
28 16 0.40
ACGTcount: A:0.24, C:0.21, G:0.32, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCCGATAAATAA
Found at i:1242744 original size:13 final size:13
Alignment explanation
Indices: 1242726--1242751 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1242716 ACAAAGATCC
1242726 ATGTATCGATACA
1 ATGTATCGATACA
1242739 ATGTATCGATACA
1 ATGTATCGATACA
1242752 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1242747 original size:33 final size:33
Alignment explanation
Indices: 1242705--1242771 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1242695 AAAATTTCCA
***
1242705 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
1242738 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
1242771 A
1 A
1242772 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:1242815 original size:19 final size:18
Alignment explanation
Indices: 1242791--1242858 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
1242781 CAGTAGCTAA
1242791 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
1242810 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
1242825 --ATGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
1242842 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
1242859 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 12 0.28
16 2 0.05
18 3 0.07
19 26 0.60
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.34
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:1242830 original size:13 final size:13
Alignment explanation
Indices: 1242812--1242838 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1242802 TACAATACTT
1242812 ATGTATCGATACA
1 ATGTATCGATACA
1242825 ATGTATCGATACA
1 ATGTATCGATACA
1242838 A
1 A
1242839 AACTTATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1242834 original size:32 final size:32
Alignment explanation
Indices: 1242793--1242857 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
1242783 GTAGCTAATT
*
1242793 ATGTATCGATACAATACTTATGTATCGATACA
1 ATGTATCGATACAAAACTTATGTATCGATACA
1242825 ATGTATCGATACAAAACTTATGTATCGATACA
1 ATGTATCGATACAAAACTTATGTATCGATACA
1242857 A
1 A
1242858 ATTGTTGAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.32
Consensus pattern (32 bp):
ATGTATCGATACAAAACTTATGTATCGATACA
Found at i:1243897 original size:15 final size:15
Alignment explanation
Indices: 1243872--1243909 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
1243862 ACTTCGGCAT
1243872 AAGTA-TTTTAGCAG
1 AAGTACTTTTAGCAG
*
1243886 AAGTACTTTTAGCAT
1 AAGTACTTTTAGCAG
1243901 AAGTACTTT
1 AAGTACTTT
1243910 GGTACAGGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 5 0.23
15 17 0.77
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.39
Consensus pattern (15 bp):
AAGTACTTTTAGCAG
Found at i:1243975 original size:15 final size:15
Alignment explanation
Indices: 1243936--1243975 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
1243926 ACACAAATAC
1243936 TTTTGGCACAAGTAT
1 TTTTGGCACAAGTAT
* * *
1243951 ATTCGACACAAGTAT
1 TTTTGGCACAAGTAT
1243966 TTTTGGCACA
1 TTTTGGCACA
1243976 TGTACTATGA
Statistics
Matches: 19, Mismatches: 6, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.35
Consensus pattern (15 bp):
TTTTGGCACAAGTAT
Found at i:1244038 original size:15 final size:15
Alignment explanation
Indices: 1243985--1244053 Score: 61
Period size: 15 Copynumber: 4.7 Consensus size: 15
1243975 ATGTACTATG
1243985 ACATAGGTA-C-TCTA
1 ACATAGGTACCTTC-A
* *
1243999 ACATAGATACTTTCA
1 ACATAGGTACCTTCA
* *
1244014 ACACAGGTACCTTCG
1 ACATAGGTACCTTCA
*
1244029 ACATAGGTACCTCCA
1 ACATAGGTACCTTCA
*
1244044 GCATAGGTAC
1 ACATAGGTAC
1244054 ATTGGTACAA
Statistics
Matches: 43, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
14 8 0.19
15 33 0.77
16 2 0.05
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (15 bp):
ACATAGGTACCTTCA
Found at i:1248345 original size:51 final size:52
Alignment explanation
Indices: 1248269--1248396 Score: 204
Period size: 51 Copynumber: 2.5 Consensus size: 52
1248259 CGAAATATGA
* *
1248269 AAATTTGCCTACATGTATCGATACATTTTATAGTGTATCGATACAT-TGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
* *
1248320 AAATTTGCCTGTACGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
1248372 AAATTTACCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
1248397 AAGATCAGTG
Statistics
Matches: 69, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
51 42 0.61
52 27 0.39
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:1248423 original size:13 final size:13
Alignment explanation
Indices: 1248405--1248429 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1248395 CAAAGATCAG
1248405 TGTATCGATACAA
1 TGTATCGATACAA
1248418 TGTATCGATACA
1 TGTATCGATACA
1248430 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1248506 original size:19 final size:19
Alignment explanation
Indices: 1248482--1248533 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
1248472 AATTGTACAT
1248482 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
*
1248501 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
1248520 TGTATCGATACAAA
1 TGTATCGATACAAA
1248534 TCGTTGAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.31
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:1253358 original size:13 final size:13
Alignment explanation
Indices: 1253340--1253367 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1253330 ATACAAAGAT
1253340 CAATGTATCGATA
1 CAATGTATCGATA
1253353 CAATGTATCGATA
1 CAATGTATCGATA
1253366 CA
1 CA
1253368 TTTCCTTGGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1253423 original size:19 final size:19
Alignment explanation
Indices: 1253399--1253494 Score: 99
Period size: 19 Copynumber: 5.7 Consensus size: 19
1253389 AGTGTTACAT
1253399 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
1253418 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
1253431 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
*
1253450 TGCATCGAT--AA-A--T-
1 TGTATCGATACAACACTTA
1253463 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
1253482 TGTATCGATACAA
1 TGTATCGATACAA
1253495 TTTCTATTTG
Statistics
Matches: 63, Mismatches: 2, Indels: 24
0.71 0.02 0.27
Matches are distributed among these distances:
13 17 0.27
14 2 0.03
15 2 0.03
16 8 0.13
17 2 0.03
18 2 0.03
19 30 0.48
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.32
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:1253435 original size:32 final size:32
Alignment explanation
Indices: 1253394--1253493 Score: 182
Period size: 32 Copynumber: 3.1 Consensus size: 32
1253384 TTCGTAGTGT
1253394 TACATTGTATCGATACAACACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
*
1253426 TACATTGTATCGATACAACACTTATGCATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
*
1253458 TAAATTGTATCGATACAACACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
1253490 TACA
1 TACA
1253494 ATTTCTATTT
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 64 1.00
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (32 bp):
TACATTGTATCGATACAACACTTATGTATCGA
Found at i:1253436 original size:13 final size:13
Alignment explanation
Indices: 1253418--1253442 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1253408 ACAACACTTA
1253418 TGTATCGATACAT
1 TGTATCGATACAT
1253431 TGTATCGATACA
1 TGTATCGATACA
1253443 ACACTTATGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1255735 original size:51 final size:51
Alignment explanation
Indices: 1255680--1255778 Score: 146
Period size: 51 Copynumber: 1.9 Consensus size: 51
1255670 TCTAACTCCA
* *
1255680 GTTTTATTTCTAAAACAACAATTTTTCACTATCG-GGGATACTCCAACCTCG
1 GTTTTATTTCTAAAACAACAATTTTCCACCAT-GAGGGATACTCCAACCTCG
* *
1255731 GTTTTATTTCTAAAACACCAATTTTCCACCATGAGGGATACTCTAACC
1 GTTTTATTTCTAAAACAACAATTTTCCACCATGAGGGATACTCCAACC
1255779 CCGTTATTTC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
50 1 0.02
51 42 0.98
ACGTcount: A:0.30, C:0.24, G:0.11, T:0.34
Consensus pattern (51 bp):
GTTTTATTTCTAAAACAACAATTTTCCACCATGAGGGATACTCCAACCTCG
Found at i:1255802 original size:79 final size:77
Alignment explanation
Indices: 1255714--1255965 Score: 249
Period size: 79 Copynumber: 3.2 Consensus size: 77
1255704 TTCACTATCG
*
1255714 GGGATACTCCAACCTCGGTTTTATTTCTAAAACACCAATTTTCCACCATGAGGGATACTCTAACC
1 GGGACACTCCAACCTCGGTTTTATTTCTAAAACACCAATTTT-CACCATGAGGGATACTCTAACC
*
1255779 CCGTTATTTCCAA
65 CCGTTATTTCCGA
* * * *
1255792 GAGGACACTCCAA-CTCTAGTTTTATTTCTAAAATATCAAATTTTCACCATCG-GGCATACTCTA
1 G-GGACACTCCAACCTC-GGTTTTATTTCTAAAACA-CCAATTTTCACCAT-GAGGGATACTCTA
* *
1255855 ACCCCTTTATTTTCGA
62 ACCCCGTTATTTCCGA
* * * * * * *
1255871 GGGGATACTCCAACCCCGATTTTATTTCTAATACACCGATTTTTCACTATCAGGGATACT-TCAA
1 -GGGACACTCCAACCTCGGTTTTATTTCTAAAACACC-AATTTTCACCATGAGGGATACTCT-AA
*
1255935 CCCCGTTATCTCCGA
63 CCCCGTTATTTCCGA
*
1255950 GGGAACATTCCAACCT
1 GGG-ACACTCCAACCT
1255966 TATTTCTTTT
Statistics
Matches: 139, Mismatches: 25, Indels: 19
0.76 0.14 0.10
Matches are distributed among these distances:
78 9 0.06
79 119 0.86
80 11 0.08
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.32
Consensus pattern (77 bp):
GGGACACTCCAACCTCGGTTTTATTTCTAAAACACCAATTTTCACCATGAGGGATACTCTAACCC
CGTTATTTCCGA
Found at i:1261099 original size:19 final size:19
Alignment explanation
Indices: 1261075--1261113 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1261065 CAATATAAAG
*
1261075 AATGAACTAATATTGAAAT
1 AATGAACTAATAATGAAAT
1261094 AATGAACTAATAATGAAAT
1 AATGAACTAATAATGAAAT
1261113 A
1 A
1261114 CTAAGTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.56, C:0.05, G:0.10, T:0.28
Consensus pattern (19 bp):
AATGAACTAATAATGAAAT
Found at i:1263907 original size:64 final size:63
Alignment explanation
Indices: 1263776--1263909 Score: 189
Period size: 63 Copynumber: 2.1 Consensus size: 63
1263766 ACTTTTTCAC
* **
1263776 TTTAATTTAGGTTTATTTTCATTAATATTTAAAAATATATATAAAAATTAAATTGGTGAAACT
1 TTTAATTTAAGTTTATTTTCATTAATATTTAAAAATATATATAAAAATTAAATTAATGAAACT
* * *
1263839 TTTAATTTAAGTTTATTTTTATTAATATTTAAAAA-ATTATATCAAAAATTAAATTAATGAGATT
1 TTTAATTTAAGTTTATTTTCATTAATATTTAAAAATA-TATAT-AAAAATTAAATTAATGAAACT
1263903 TTTAATT
1 TTTAATT
1263910 AGTCGTAAGA
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
62 1 0.02
63 38 0.60
64 24 0.38
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (63 bp):
TTTAATTTAAGTTTATTTTCATTAATATTTAAAAATATATATAAAAATTAAATTAATGAAACT
Found at i:1264184 original size:16 final size:15
Alignment explanation
Indices: 1264161--1264190 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1264151 TAATTTTAAT
1264161 ATTAAATAAATATTA
1 ATTAAATAAATATTA
1264176 ATTATAATAAATATT
1 ATTA-AATAAATATT
1264191 TAATAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
ATTAAATAAATATTA
Found at i:1264201 original size:17 final size:17
Alignment explanation
Indices: 1264147--1264209 Score: 60
Period size: 17 Copynumber: 3.8 Consensus size: 17
1264137 TAATTATATT
1264147 AAAAT-AAT-TTTAATA
1 AAAATAAATATTTAATA
* *
1264162 TTAAATAAATA-TTAATT
1 -AAAATAAATATTTAATA
*
1264179 ATAATAAATATTTAATA
1 AAAATAAATATTTAATA
*
1264196 AAAATATATATTTA
1 AAAATAAATATTTA
1264210 GTTAAATGAT
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
16 12 0.32
17 25 0.68
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AAAATAAATATTTAATA
Found at i:1265615 original size:20 final size:20
Alignment explanation
Indices: 1265586--1265625 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1265576 TTTTATTTTT
*
1265586 AAATTTTATATATATTTAAA
1 AAATTATATATATATTTAAA
1265606 AAATTATATATATATTTAAA
1 AAATTATATATATATTTAAA
1265626 TATGCATAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AAATTATATATATATTTAAA
Found at i:1266753 original size:14 final size:14
Alignment explanation
Indices: 1266736--1266784 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
1266726 AAAAATAAAA
1266736 AATATTTTTATATT
1 AATATTTTTATATT
*
1266750 AATATTTATAT-TT
1 AATATTTTTATATT
1266763 ATATATTTTTATAATT
1 A-ATATTTTTAT-ATT
1266779 AA-ATTT
1 AATATTT
1266785 AAATAATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
13 3 0.10
14 23 0.77
15 1 0.03
16 3 0.10
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
AATATTTTTATATT
Found at i:1274634 original size:20 final size:20
Alignment explanation
Indices: 1274609--1274661 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
1274599 AACATGATAT
*
1274609 AAAAATAATATAGACATG-CA
1 AAAAAT-ATATAAACATGTCA
1274629 AAAAATATATAAACATGTCA
1 AAAAATATATAAACATGTCA
* *
1274649 AAATATACATAAA
1 AAAAATATATAAA
1274662 ATAAATTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 10 0.34
20 19 0.66
ACGTcount: A:0.62, C:0.09, G:0.06, T:0.23
Consensus pattern (20 bp):
AAAAATATATAAACATGTCA
Found at i:1275497 original size:16 final size:17
Alignment explanation
Indices: 1275476--1275520 Score: 74
Period size: 17 Copynumber: 2.7 Consensus size: 17
1275466 ATTAATATGT
1275476 AAAATTTATATA-GTAA
1 AAAATTTATATATGTAA
1275492 AAAATTTATATATGTAA
1 AAAATTTATATATGTAA
*
1275509 AAAATTAATATA
1 AAAATTTATATA
1275521 ATATTTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
16 12 0.44
17 15 0.56
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (17 bp):
AAAATTTATATATGTAA
Found at i:1281928 original size:20 final size:20
Alignment explanation
Indices: 1281903--1281953 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
1281893 GTTGGGGACA
** * *
1281903 ATGTATCGATACTTTTTACT
1 ATGTATCGATACAATGTACC
1281923 ATGTATCGATACAATGTACC
1 ATGTATCGATACAATGTACC
1281943 ATGTATCGATA
1 ATGTATCGATA
1281954 TATTTCACTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACAATGTACC
Done.